Using artificial intelligence to risk stratify COVID-19 patients based on chest X-ray findings

Background: Deep learning-based radiological image analysis could facilitate use of chest x-rays as a triaging tool for COVID-19 diagnosis in resource-limited settings. This study sought to determine whether a modified commercially available deep learning algorithm (M-qXR) could risk stratify patients with suspected COVID-19 infections. Methods: A dual track clinical validation study was designed to assess the clinical accuracy of M-qXR. The algorithm evaluated all Chest-X-rays (CXRs) performed during the study period for abnormal findings and assigned a COVID-19 risk score. Four independent radiologists served as radiological ground truth. The M-qXR algorithm output was compared against radiological ground truth and summary statistics for prediction accuracy were calculated. In addition, patients who underwent both PCR testing and CXR for suspected COVID-19 infection were included in a co-occurrence matrix to assess the sensitivity and specificity of the M-qXR algorithm. Results: 625 CXRs were included in the clinical validation study. 98% of total interpretations made by M-qXR agreed with ground truth (p = 0.25). M-qXR correctly identified the presence or absence of pulmonary opacities in 94% of CXR interpretations. M-qXR's sensitivity, specificity, PPV, and NPV for detecting pulmonary opacities were 94%, 95%, 99%, and 88% respectively. M-qXR correctly identified the presence or absence of pulmonary consolidation in 88% of CXR interpretations (p = 0.48). M-qXR's sensitivity, specificity, PPV, and NPV for detecting pulmonary consolidation were 91%, 84%, 89%, and 86% respectively. Furthermore, 113 PCR-confirmed COVID-19 cases were used to create a co-occurrence matrix between M-qXR's COVID-19 risk score and COVID-19 PCR test results. The PPV and NPV of a medium to high COVID-19 risk score assigned by M-qXR yielding a positive COVID-19 PCR test result was estimated to be 89.7% and 80.4% respectively. Conclusion: M-qXR was found to have comparable accuracy to radiological ground truth in detecting radiographic abnormalities on CXR suggestive of COVID-19

Complicaciones de la colocación de malla sintética vaginal para la incontinencia urinaria de esfuerzo

ResumenAntecedentesLas mallas para la incontinencia urinaria (IU) se han utilizado a pesar de la falta de evidencia de nivel i en la literatura para evaluar su seguridad y eficacia a largo plazo. Las complicaciones relacionadas con la malla provocaron una advertencia emitida por la FDA en 2008 y dejaron de ser consideradas eventos raros. Las complicaciones más comunes son la retención aguda de orina, sangrado, recurrencia o persistencia de la IU, erosión de uretra e infección de la malla.ObjetivoConocer cuáles son las complicaciones derivadas del tratamiento quirúrgico de la IU femenina con la colocación de mallas suburetrales.Material y métodoSe analizaron los pacientes con diagnóstico de IU operadas con cirugía antiincontinencia y colocación de malla vaginal del año 2007 al 2014. Se analizó las complicaciones derivadas de la colocación de malla y la recuperación de continencia.ResultadosA 58 pacientes se les colocó sling (cabestrillo) con malla sintética; edad promedio de 56 años. El 51% de las pacientes tenían IU de esfuerzo y el 49% IU mixta. Las complicaciones tempranas fueron: 4 pacientes con retención aguda de orina. Las complicaciones tardías: dolor uretral o vaginal (12.2%), dispareunia (20%) y extrusión de malla (10%) manejado con retiro de la misma, 2 de ellas requiriendo 2 procedimientos quirúrgicos. El 12% presentaron urgencia de novo, el 90.2% evolucionaron sin incontinencia, el 9.7% con IU postoperatoria y 2 pacientes sin mejoría.DiscusiónNuestra serie, aunque pequeña, muestra una baja tasa de complicaciones a largo plazo relacionadas con la malla en comparación con la mayoría de las series que muestran una tasa de reoperación de hasta>70% y con múltiples casos de retiro de malla, por lo que en nuestra experiencia los slings suburetrales continúan siendo una opción adecuada en el manejo de la IU.ConclusionesLos slings suburetrales son una opción segura y efectiva en el manejo de la IU.AbstractBackgroundSurgical mesh has been used for treating urinary incontinence (UI) despite the lack of level i evidence in the literature evaluating its long-term safety and efficacy. Mesh-related complications were responsible for a warning issued by the FDA in 2008 and they stopped being considered rare events. The most common complications are acute urinary retention, bleeding, recurrence or persistence of UI, erosion of the urethra, and mesh infection.AimsTo determine the complications derived from surgical UI treatment with the placement of suburethral mesh in women.Material and methodPatients diagnosed with UI that underwent anti-incontinence surgery with the placement of vaginal mesh within the time frame of 2007 and 2014 were analyzed. Mesh placement complications and the recovery of continence were evaluated.ResultsA synthetic mesh sling was placed in 58 patients with a mean age of 56 years. A total of 51% of the patients had stress urinary incontinence and 49% had mixed urinary incontinence. Early complications were: 4 patients with acute urine retention. Late complications were: urethral or vaginal pain (12.2%), dyspareunia (20%), and mesh extrusion (10%) that was managed through mesh removal; 2 of those patients required surgical procedures. Twelve percent of the patients presented with de novo urgency, 90.2% progressed with no incontinence, 9.7% presented with postoperative UI, and 2 patients had no improvement.DiscussionAlthough small, our case series showed a low long-term complication rate with the use of surgical mesh, compared with the majority of case series that demonstrate a re-operation rate>70%, as well as numerous cases of mesh removal. Thus, it is our experience that suburethral slings continue to be an adequate UI management option.ConclusionsSuburethral slings are a safe and effective option in UI management

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Native diversity buffers against severity of non-native tree invasions

Determining the drivers of non-native plant invasions is critical for managing native ecosystems and limiting the spread of invasive species1,2. Tree invasions in particular have been relatively overlooked, even though they have the potential to transform ecosystems and economies3,4. Here, leveraging global tree databases5–7, we explore how the phylogenetic and functional diversity of native tree communities, human pressure and the environment influence the establishment of non-native tree species and the subsequent invasion severity. We find that anthropogenic factors are key to predicting whether a location is invaded, but that invasion severity is underpinned by native diversity, with higher diversity predicting lower invasion severity. Temperature and precipitation emerge as strong predictors of invasion strategy, with non-native species invading successfully when they are similar to the native community in cold or dry extremes. Yet, despite the influence of these ecological forces in determining invasion strategy, we find evidence that these patterns can be obscured by human activity, with lower ecological signal in areas with higher proximity to shipping ports. Our global perspective of non-native tree invasion highlights that human drivers influence non-native tree presence, and that native phylogenetic and functional diversity have a critical role in the establishment and spread of subsequent invasions

Partitioning the Heritability of Tourette Syndrome and Obsessive Compulsive Disorder Reveals Differences in Genetic Architecture

The direct estimation of heritability from genome-wide common variant data as implemented in the program Genome-wide Complex Trait Analysis (GCTA) has provided a means to quantify heritability attributable to all interrogated variants. We have quantified the variance in liability to disease explained

Phylogenomics and the rise of the angiosperms

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5,6,7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade

One sixth of Amazonian tree diversity is dependent on river floodplains

Amazonia's floodplain system is the largest and most biodiverse on Earth. Although forests are crucial to the ecological integrity of floodplains, our understanding of their species composition and how this may differ from surrounding forest types is still far too limited, particularly as changing inundation regimes begin to reshape floodplain tree communities and the critical ecosystem functions they underpin. Here we address this gap by taking a spatially explicit look at Amazonia-wide patterns of tree-species turnover and ecological specialization of the region's floodplain forests. We show that the majority of Amazonian tree species can inhabit floodplains, and about a sixth of Amazonian tree diversity is ecologically specialized on floodplains. The degree of specialization in floodplain communities is driven by regional flood patterns, with the most compositionally differentiated floodplain forests located centrally within the fluvial network and contingent on the most extraordinary flood magnitudes regionally. Our results provide a spatially explicit view of ecological specialization of floodplain forest communities and expose the need for whole-basin hydrological integrity to protect the Amazon's tree diversity and its function.Naturali

Integrated global assessment of the natural forest carbon potential

Forests are a substantial terrestrial carbon sink, but anthropogenic changes in land use and climate have considerably reduced the scale of this system1. Remote-sensing estimates to quantify carbon losses from global forests2,3,4,5 are characterized by considerable uncertainty and we lack a comprehensive ground-sourced evaluation to benchmark these estimates. Here we combine several ground-sourced6 and satellite-derived approaches2,7,8 to evaluate the scale of the global forest carbon potential outside agricultural and urban lands. Despite regional variation, the predictions demonstrated remarkable consistency at a global scale, with only a 12% difference between the ground-sourced and satellite-derived estimates. At present, global forest carbon storage is markedly under the natural potential, with a total deficit of 226 Gt (model range = 151–363 Gt) in areas with low human footprint. Most (61%, 139 Gt C) of this potential is in areas with existing forests, in which ecosystem protection can allow forests to recover to maturity. The remaining 39% (87 Gt C) of potential lies in regions in which forests have been removed or fragmented. Although forests cannot be a substitute for emissions reductions, our results support the idea2,3,9 that the conservation, restoration and sustainable management of diverse forests offer valuable contributions to meeting global climate and biodiversity targets

Native diversity buffers against severity of non-native tree invasions

Determining the drivers of non-native plant invasions is critical for managing native ecosystems and limiting the spread of invasive species1,2. Tree invasions in particular have been relatively overlooked, even though they have the potential to transform ecosystems and economies3,4. Here, leveraging global tree databases5–7, we explore how the phylogenetic and functional diversity of native tree communities, human pressure and the environment influence the establishment of non-native tree species and the subsequent invasion severity. We find that anthropogenic factors are key to predicting whether a location is invaded, but that invasion severity is underpinned by native diversity, with higher diversity predicting lower invasion severity. Temperature and precipitation emerge as strong predictors of invasion strategy, with non-native species invading successfully when they are similar to the native community in cold or dry extremes. Yet, despite the influence of these ecological forces in determining invasion strategy, we find evidence that these patterns can be obscured by human activity, with lower ecological signal in areas with higher proximity to shipping ports. Our global perspective of non-native tree invasion highlights that human drivers influence non-native tree presence, and that native phylogenetic and functional diversity have a critical role in the establishment and spread of subsequent invasions